oligotm - Prints oligo's melting temperature on stdout

       Copyright © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical
       Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky

       All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the
       licence of oligotm.

       This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be
       used by others). Permission is granted to copy, distribute and/or modify this document under the same
       terms as oligotm itself.

oligotm 1.1.4                                      11/30/2011                                         OLIGOTM(1)

oligotm prints the melting temperature of a given deoxyribonucleotide on the standard output. It is part
       of the oligotm library.

       oligotm - Prints oligo's melting temperature on stdout

-mvmonovalent_conc
           Concentration of monovalent cations in mM, by default 50 mM.

       -dvdivalent_conc
           Concentration of divalent cations in mM, by default 0 mM.

       -ndNTP_conc
           Concentration of deoxynucleotide triphosphate in mM, by default 0 mM.

       -ddna_conc
           Concentration of DNA strands in nM, by default 50 nM.

       -tp[0|1]
           Specifies the table of thermodynamic parameters and the method of melting temperature calculation:

           •   0 Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release
               1.1.0). This is the default, but not the recommended value.

           •   1 Use nearest neighbor parameter from SantaLucia 1998.  Thisistherecommendedvalue.

       -sc[0..2]
           Specifies salt correction formula for the melting temperature calculation:

           •   0 Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the
               default, but not the recommended value.

           •   1 SantaLucia 1998.  Thisistherecommendedvalue.

           •   2 Owczarzy et al., 2004.

       -i
           prints references to publications which were used for thermodynamic calculations.

       Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist
       programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series
       Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.

primer3_core(1) ntdpal(1)

oligotm [OPTIONS] {oligo}

       where oligo is a DNA sequence of between 2 and 36 bases